Century-of-Information Research (CIR): a strategy for research and innovation in the century of information

More data will be produced in the next five years than in the entire history of human kind, a digital deluge that marks the beginning of the Century of Information. Through a year-long consultation with UK researchers, a coherent strategy has been developed, which will nurture Century-of-Information Research (CIR); it crystallises the ideas developed by the e-Science Directors' Forum Strategy Working Group. This paper is an abridged version of their latest report which can be found at: http://wikis.nesc.ac.uk/escienvoy/Century_of_Information_Research_Strategy which also records the consultation process and the affiliations of the authors. This document is derived from a paper presented at the Oxford e-Research Conference 2008 and takes into account suggestions made in the ensuing panel discussion. The goals of the CIR Strategy are to facilitate the growth of UK research and innovation that is data and computationally intensive and to develop a new culture of 'digital-systems judgement' that will equip research communities, businesses, government and society as a whole, with the skills essential to compete and prosper in the Century of Information. The CIR Strategy identifies a national requirement for a balanced programme of coordination, research, infrastructure, translational investment and education to empower UK researchers, industry, government and society. The Strategy is designed to deliver an environment which meets the needs of UK researchers so that they can respond agilely to challenges, can create knowledge and skills, and can lead new kinds of research. It is a call to action for those engaged in research, those providing data and computational facilities, those governing research and those shaping education policies. The ultimate aim is to help researchers strengthen the international competitiveness of the UK research base and increase its contribution to the economy. The objectives of the Strategy are to better enable UK researchers across all disciplines to contribute world-leading fundamental research; to accelerate the translation of research into practice; and to develop improved capabilities, facilities and context for research and innovation. It envisages a culture that is better able to grasp the opportunities provided by the growing wealth of digital information. Computing has, of course, already become a fundamental tool in all research disciplines. The UK e-Science programme (2001-06)—since emulated internationally—pioneered the invention and use of new research methods, and a new wave of innovations in digital-information technologies which have enabled them. The Strategy argues that the UK must now harness and leverage its own, plus the now global, investment in digital-information technology in order to spread the benefits as widely as possible in research, education, industry and government. Implementing the Strategy would deliver the computational infrastructure and its benefits as envisaged in the Science & Innovation Investment Framework 2004-2014 (July 2004), and in the reports developing those proposals. To achieve this, the Strategy proposes the following actions: support the continuous innovation of digital-information research methods; provide easily used, pervasive and sustained e-Infrastructure for all research; enlarge the productive research community which exploits the new methods efficiently; generate capacity, propagate knowledge and develop skills via new curricula; and develop coordination mechanisms to improve the opportunities for interdisciplinary research and to make digital-infrastructure provision more cost effective. To gain the best value for money strategic coordination is required across a broad spectrum of stakeholders. A coherent strategy is essential in order to establish and sustain the UK as an international leader of well-curated national data assets and computational infrastructure, which is expertly used to shape policy, support decisions, empower researchers and to roll out the results to the wider benefit of society. The value of data as a foundation for wellbeing and a sustainable society must be appreciated; national resources must be more wisely directed to the collection, curation, discovery, widening access, analysis and exploitation of these data. Every researcher must be able to draw on skills, tools and computational resources to develop insights, test hypotheses and translate inventions into productive use, or to extract knowledge in support of governmental decision making. This foundation plus the skills developed will launch significant advances in research, in business, in professional practice and in government with many consequent benefits for UK citizens. The Strategy presented here addresses these complex and interlocking requirements.

Gas phase kinetic and quantum chemical studies of the reactions of silylene with the methylsilanes. Absolute rate constants, temperature dependences, RRKM modelling and potential energy surfaces

Time resolved studies of silylene, SiH2, generated by the 193 nm laser. ash photolysis of phenylsilane, have been carried out to obtain rate coefficients for its bimolecular reactions with methyl-, dimethyl- and trimethyl-silanes in the gas phase. The reactions were studied over the pressure range 3 - 100 Torr with SF6 as bath gas and at five temperatures in the range 300 - 625 K. Only slight pressure dependences were found for SiH2 + MeSiH3 ( 485 and 602 K) and for SiH2 + Me2SiH2 ( 600 K). The high pressure rate constants gave the following Arrhenius parameters: [GRAPHICS] These are consistent with fast, near to collision-controlled, association processes. RRKM modelling calculations are consistent with the observed pressure dependences ( and also the lack of them for SiH2 + Me3SiH). Ab initio calculations at both second order perturbation theory (MP2) and coupled cluster (CCSD(T)) levels, showed the presence of weakly-bound complexes along the reaction pathways. In the case of SiH2 + MeSiH3 two complexes, with different geometries, were obtained consistent with earlier studies of SiH2 + SiH4. These complexes were stabilised by methyl substitution in the substrate silane, but all had exceedingly low barriers to rearrangement to product disilanes. Although methyl groups in the substrate silane enhance the intrinsic SiH2 insertion rates, it is doubtful whether the intermediate complexes have a significant effect on the kinetics. A further calculation on the reaction MeSiH + SiH4 shows that the methyl substitution in the silylene should have a much more significant kinetic effect ( as observed in other studies).

MPJ express: Towards thread safe Java HPC

MPJ Express is a thread-safe Java messaging library that provides a full implementation of the mpiJava 1.2 API specification. This specification defines a MPI-like bindings for the Java language. We have implemented two communication devices as part of our library, the first, called niodev is based on the Java New I/O package and the second, called mxdev is based on the Myrinet eXpress library MPJ Express comes with an experimental runtitne, which allows portable bootstrapping of Java Virtual Machines across a cluster or network of computers. In this paper we describe the implementation of MPJ Express. Also, we present a performance comparison against various other C and Java messaging systems. A beta version of MPJ Express was released in September 2005.

MPJ express meets gadget: towards a java code for cosmological simulations

Gadget-2 is a massively parallel structure formation code for cosmological simulations. In this paper, we present a Java version of Gadget-2. We evaluated the performance of the Java version by running colliding galaxies simulation and found that it can achieve around 70% of C Gadget-2's performance.

A buffering layer to support derived types and proprietary networks for Java HPC

MPJ Express is our implementation of MPI-like bindings for Java. In this paper we discuss our intermediate buffering layer that makes use of the so-called direct byte buffers introduced in the Java New I/O package. The purpose of this layer is to support the implementation of derived datatypes. MPJ Express is the first Java messaging library that implements this feature using pure Java. In addition, this buffering layer allows efficient implementation of communication devices based on proprietary networks such as Myrinet. In this paper we evaluate the performance of our buffering layer and demonstrate the usefulness of direct byte buffers. Also, we evaluate the performance of MPJ Express against other messaging systems using Myrinet and show that our buffering layer has made it possible to avoid the overheads suffered by other Java systems such as mpiJava that relies on the Java Native Interface.

A buffering layer to support derived types and proprietary networks for Java HPC

MPJ Express is our implementation of MPI-like bindings for Java. In this paper we discuss our intermediate buffering layer that makes use of the so-called direct byte buffers introduced in the Java New I/O package. The purpose of this layer is to support the implementation of derived datatypes. MPJ Express is the first Java messaging library that implements this feature using pure Java. In addition, this buffering layer allows efficient implementation of communication devices based on proprietary networks such as Myrinet. In this paper we evaluate the performance of our buffering layer and demonstrate the usefulness of direct byte buffers. Also, we evaluate the performance of MPJ Express against other messaging systems using Myrinet and show that our buffering layer has made it possible to avoid the overheads suffered by other Java systems such as mpiJava that relies on the Java Native Interface.

Nested parallelism for multi-core HPC systems using Java

Since its introduction in 1993, the Message Passing Interface (MPI) has become a de facto standard for writing High Performance Computing (HPC) applications on clusters and Massively Parallel Processors (MPPs). The recent emergence of multi-core processor systems presents a new challenge for established parallel programming paradigms, including those based on MPI. This paper presents a new Java messaging system called MPJ Express. Using this system, we exploit multiple levels of parallelism - messaging and threading - to improve application performance on multi-core processors. We refer to our approach as nested parallelism. This MPI-like Java library can support nested parallelism by using Java or Java OpenMP (JOMP) threads within an MPJ Express process. Practicality of this approach is assessed by porting to Java a massively parallel structure formation code from Cosmology called Gadget-2. We introduce nested parallelism in the Java version of the simulation code and report good speed-ups. To the best of our knowledge it is the first time this kind of hybrid parallelism is demonstrated in a high performance Java application. (C) 2009 Elsevier Inc. All rights reserved.

A comparative study of Java and C performance in two large-scale parallel applications

In the 1990s the Message Passing Interface Forum defined MPI bindings for Fortran, C, and C++. With the success of MPI these relatively conservative languages have continued to dominate in the parallel computing community. There are compelling arguments in favour of more modern languages like Java. These include portability, better runtime error checking, modularity, and multi-threading. But these arguments have not converted many HPC programmers, perhaps due to the scarcity of full-scale scientific Java codes, and the lack of evidence for performance competitive with C or Fortran. This paper tries to redress this situation by porting two scientific applications to Java. Both of these applications are parallelized using our thread-safe Java messaging system—MPJ Express. The first application is the Gadget-2 code, which is a massively parallel structure formation code for cosmological simulations. The second application uses the finite-domain time-difference method for simulations in the area of computational electromagnetics. We evaluate and compare the performance of the Java and C versions of these two scientific applications, and demonstrate that the Java codes can achieve performance comparable with legacy applications written in conventional HPC languages. Copyright © 2009 John Wiley & Sons, Ltd.

Assessing the impact of nano- and micro-scale zerovalent iron particles on soil microbial activities: Particle reactivity interferes with assay conditions and interpretation of genuine microbial effects

The effects of nano-scale and micro-scale zerovalent iron (nZVI and mZVI) particles on general (dehydrogenase and hydrolase) and specific (ammonia oxidation potential, AOP) activities mediated by the microbial community in an uncontaminated soil were examined. nZVI (diameter 12.5 nm; 10 mg gÿ1 soil)apparently inhibited AOP and nZVI and mZVI apparently stimulated dehydrogenase activity but had minimal influence on hydrolase activity. Sterile experiments revealed that the apparent inhibition of AOP could not be interpreted as such due to the confounding action of the particles, whereas, the nZVIenhanced dehydrogenase activity could represent the genuine response of a stimulated microbial population or an artifact of ZVI reactivity. Overall, there was no evidence for negative effects of nZVI or mZVI on the processes studied. When examining the impact of redox active particles such as ZVI on microbial oxidation–reduction reactions, potential confounding effects of the test particles on assay conditions should be considered.